Projects
Short Research Projects
The EngBio Cohort 1 students worked on two 11-week projects during their taught year. These projects were inter-disciplinary and aligned with the four major Engineering Biology research areas:
- Robust methods for bioengineering
- Rational biomolecular & biosystems design
- Evolution-guided biodesign
- Digital cells & AI
Typically, one of these short projects have now been developed into the substantive DPhil (Oxford) or PhD (Bristol) project that students will work on throughout years two to four.
Details of these projects are below.
Cohort 1 (2024 entry)
Mr James Bridson
Cohort 1 (Oxford)
Project 1 – Oxygen-dependent protein degradation in plants (Francesco Licausi)
Project 2 – Reducing leak in rhizopine-inducible systems for applications in engineering nitrogen fixation (Philip Poole, Antonis Papachristadoulou)
DPhil – Engineering Control of Nitrogen Fixation in Free-Living Diazotrophs for Application on Cereal Crops (Philip Poole, Antonis Papachristodoulou)
Mr Felipe Xavier Buson
Cohort 1 (Bristol)
Project 1 – Exploring novel strategies for transcriptional termination in RNA-based genetic circuits (Thomas Gorochowski, Jonathan Bath)
Project 2 – Towards inducible liquid-liquid phase separation with modular de-novo designed proteins (Andrey Romanyuk, Dek Woolfson)
Miss Yige Chen
Cohort 1 (Bristol)
Project 1 – Generative AI-driven reduced genome design (Lucia Marucci, Claire Grierson, Zahraa Abdullah)
Project 2 – Soft-Material Well Plates with Pneumatic Actuation for Gut-on-a-Chip Applications (Ryman Hashem, Pablo Cespedes Donoso, Lei Wu, Jonathan Rossiter)
Mr Jack Dalton
Cohort 1 (Oxford)
Project 1 – Applying directed evolution to extremophiles for biomanufacturing and terraforming (Harrison Steel, Jean-Baptiste Lugagne)
Project 2 – Using reinforcement learning to understand protein expression (Jean-Baptiste Lugagne)
DPhil – Engineering Evolution: Optimisation of biological systems for biomanufacturing using automated adaptive evolution and machine learning (Harrison Steel, Jean-Baptiste Lugagne)
Miss Cecilia Gallego Rubio
Cohort 1 (Oxford)
Project 1 – Engineering T cells with synthetic co-signalling receptors for modulated antigen cross-reactivity (Jose Cabezas Caballero, Omer Dushek)
Project 2 – Progress towards isothermal competitive amplification netwroks with lateral flow output (Chaewon Park, Jonathan Bath, Molly Stevens)
DPhil Project – Developing an RPA-based competitive amplification network and translation into a lateral flow output for a diagnostic platform (Molly Stevens, Jonathan Bath)
Mr Johan Guillen Meza
Cohort 1 (Bristol)
Project 1 – Accelerating the engineering of bacterial cells as optimal production strains for metabolic engineering via Whole-Cell Modelling and Machine Learning (Claire Grierson, Lucia Marucci)
Project 2 – Design of a Light-Sensitive Circuit in E.coli to perform Physical Reservoir Computing (Thomas Gorochowski, Helmut Hauser)
Mr Robin Henry
Cohort 1 (Oxford)
Project 1 – Control of gene expression in single cells using advance real-time control algorithms (Jean-Baptiste Lugagne, Harrison Steel)
Project 2 – Identification and experimental testing of fast-responding sub-cellular reporters for magnetogenetic actuation (Harrison Steel, Jean-Baptiste Lugagne)
DPhil – Next-Generation Experimental Platforms for Learning from Single Cells (Jean-Baptiste Lugagne, Harrison Steel)
Mr Sam Kemery
Cohort 1 (Bristol)
Project 1 – D-NEMD and MD analysis of the structure and dynamics of a series of artificially evolved Magneto-sensitive Fluorescent Proteins derived from the A.sativa LOV2 domain (Adrian Mulholland, Sofia Oliveira)
Project 2 – Structural and biophysical characterisation of an artificially evolved series of Magneto-sensitive Fluorescent Proteins derived from the A.sativa LOV2 domain (Ross Anderson)
Miss Natasha Kisseroudis
Position
Project 1 – Building a minimally viable vascular structure using two-photo polymerisation (2PP) 3D printing and subtractive manufacturing (Matteo Albino, Patrick Peschke, Alex Pascual-Cid, Malavika Nair, Dario Carugo, Jonathan P Wojciechowski, Molly Stevens)
Project 2 – A minimal vascular model for cell survival in a perfused scaffold bioreactor (Samantha Baker-Jones, James Fisk, Joel Balkaran, Matthew Burgess, Ryan Murray, Dario Carugo, Malavika Nair)
DPhil Project – Designing and building a vascular platform using subtractive manufacturing, for applications in Engineering Biology (e.g. tissue engineering, engineered living materials, robotics). (Liang He, Molly Stevens)
Mr Gil Krikler
Cohort 1 (Bristol)
Project 1 – Engineered sickle-cells as vectors for tumour-targeted cancer therapeutics (Ash Toye)
Project 2 – Analysing Dynamics of LLPS in Viscous Environments (Yutong Fu, Jennifer McManus)
Miss Lucy Slater
Cohort 1 (Oxford)
Project 1 – Investigating the effect of steroid dosage on the behaviour of oncolytic viruses in liver tissue and cells (Robert Carlisle, David Johnson)
Project 2 – The Impact of Aversive Context on Behaviour and Pain Perception in Virtual Reality (Timothy Denison, Shuangyi Tong, Ben Seymour)
DPhil – Smart Adaptive Virtual Reality: using closed-loop paradigms that combine computational analysis of real-time behavioural and physiological data (Ben Seymour, Tim Denison)
Miss Maria Tasca
Cohort 1 (Bristol)
Project 1 – Multicellular compositional control of cellular consortia in mammalian cells (Martin Homer, Lucia Marucci)
Project 2 – Host-aware models of evolution in engineered cell communities (Thomas Gorochowski, Claire Grierson)
Mr Colin Veale
Cohort 1 (Oxford)
Project 1 – Engineering therapeutic TCRs against EWS-FLI-1 for Ewing Sarcoma (Malcolm Sim, Tim Elliot, Tanusya Murali)
Project 2 – Increasing the speciality of engineered T-cell receptor therapies targeting cancer (Kirtana Sivasubramanian, Jose Cabezas Cabellero, Anton van der Merwe, Omer Dushek)
DPhil Project – Engineering synthetic bi-specific molecules to reduce autoimmune toxicities in T cell immunotherapies (Robert Carlisle, Omer Dushek, Malcolm Sim)
EPSRC & BBSRC Centre for Doctoral Training in Engineering Biology (EngBio CDT)
University of Bristol
School of Engineering Mathematics and Technology
Tankard’s Close
Bristol, BS8 1TW
University of Oxford
Department of Engineering Science, Botnar Research Centre, Old Road, Headington, Oxford, OX3 7LD
